Heat effect of laser medium can cause the aberration of the laser in the process of operation, resulting in the decrease of the laser beam quality, and seriously affecting the development and application of the solid-laser. A three-dimensional physical model of a double-side fluid cooling system with microchannel structure is established in the present work. Flow, temperature and Nd∶YAG crystal slices′s stress fields of the cooling system are simulated, and effects of Reynolds number and heat flux inside crystal slice on thermal deformation of the slice are investigated with fluid-solid coupling method. Results show that the flow field significantly influences temperature and stress fields of the crystal slice. The maximum Von Mises equivalent stress decreases with the increase of the Reynolds number, and its maximum value is located at the edge of the slice. There are different distributions of the thermal deformation under different flow conditions. The heat flux is found to only affect the extent of the thermal deformation, the higher the heat flux, the more obvious the thermal deformation.